On the Keweenaw Peninsula of Lake Superior, two stamp mills (Mohawk and Wolverine) discharged 22.7 million metric tonnes (MMT) of tailings (1901–1932) into the coastal zone off the town of Gay. Migrating along the shoreline, ca. 10 MMT of the tailings dammed stream and river outlets, encroached upon wetlands, and contaminated recreational beaches. A nearly equal amount of tailings moved across bay benthic environments into critical commercial fish spawning and rearing grounds. In the middle of the bay, Buffalo Reef is important for commercial and recreational lake trout and lake whitefish production (ca. 32% of the commercial catch in Keweenaw Bay, 22% along southern Lake Superior). Aerial photographs (1938–2016) and five LiDAR and multispectral over-flights (2008–2016) emphasize: (1) the enormous amounts of tailings moving along the beach; and (2) the bathymetric complexities of an equal amount migrating underwater across the shelf. However, remote sensing studies encounter numerous specific challenges in coastal environments. Here, we utilize a combination of elevation data (LiDAR digital elevation/bathymetry models) and in situ studies to generate a series of physical, chemical, and biological geospatial maps. The maps are designed to help assess the impacts of historical mining on Buffalo Reef. Underwater, sand mixtures have complicated multispectral bottom reflectance substrate classifications. An alternative approach, in situ simple particle classification, keying off distinct sand end members: (1) allows calculation of tailings (stamp sand) percentages; (2) aids indirect and direct assays of copper concentrations; and (3) permits determinations of density effects on benthic macro-invertebrates. The geospatial mapping shows how tailings are moving onto Buffalo Reef, the copper concentrations associated with the tailings, and how both strongly influence the density of benthic communities, providing an excellent example for the International Maritime Organization on how mining may influence coastal reefs. We demonstrate that when large amounts of mine tailings are discharged into coastal environments, temporal and spatial impacts are progressive, and strongly influence resident organisms. Next steps are to utilize a combination of hi-resolution LiDAR and sonar surveys, a fish-monitoring array, and neural network analysis to characterize the geometry of cobble fields where fish are successful or unsuccessful at producing young.